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Host-associated Microbiota

Daphnia with bacteria

Bacteria on our main study organism, Daphnia magna. EM pictures by Frida Ben-Ami.

Part of the work in the Ebert group concerns the evolution and ecology of host-associated microbiota. We address this topic from a conceptual prespective and conduct empirical research on the microbiota of the zooplanktonic crustaceans of the genus Daphnia. Here you find some information about this microbiota project and the people involved in it.


Microbial communities (=microbiota) associated with multicellular organisms play an important role in host nutrition and development. Advances in sequencing technology have revealed an unexpectedly high diversity of microbiota; These advances are not, however, matched by advances in our understanding of the evolutionary factors that structure microbiota. The goal of our research is to fill this knowledge gap.

Evolutionary models developed for simple host-symbiont relationships have identified a number of factors that shape these relationships: mode of transmission (horizontal versus maternal transmission), host ranges and fitness effects for the host. Together these factors influence the role of selection among hosts and the role of selection within hosts (among microbes), the two levels of selection that are believed to shape host-symbiont coevolution. We intend to expand these models to host-microbiota interactions. Our objectives are to use next-generation sequencing to conduct a comparative study of bacterial microbiota structure and to combine this work with experiments that explore the underlying evolutionary processes.

We focus on the crustacean family Daphniidae (mainly the genus Daphnia), a system ideally suited for studies in the field and laboratory. We test hypotheses about the evolution of mutualism, virulence, cheating and coevolution, as well as test for the role of mode of transmission and host specificity. The analysis of host-microbiota associations is conducted for entire microbiota and for stepwise simplified, but biologically meaningful subsets. Testing general models for the evolution of microbiota will have implications far beyond the chosen model system, ranging from ecology and evolution to agricultural sciences and medicine.

This project is supported by an advanced investigator grant of the European Research Council (ERC).

Other activities

In September 2012, we hosted a workshop on "Host-associated Microbiota" at Basel University. For more information on this memorable event go here: Host-associated Microbiota workshop.